SMTL ID : 4ax9.1

Human thrombin complexed with Napsagatran, RO0466240

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-1-mer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: K.174, T.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.174 NA.2: 2 residues within 4Å: Chain A: R.233, K.236 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.236, A:K.236 Water bridges: A:R.197, A:G.238

1 x N5N: 2-[[(2S)-4-[[(3S)-1-carbamimidoylpiperidin-3-yl]methylamino]-2-(naphthalen-2-ylsulfonylamino)-4-oxidanylidene-butanoyl] -cyclopropyl-amino]ethanoic acid(Non-covalent)

N5N.3: 19 residues within 4Å: Chain A: H.43, Y.47, W.50, E.94, N.95, L.96, D.199, A.200, C.201, E.202, S.205, V.225, S.226, W.227, G.228, E.229, G.230, C.231, G.238 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.47, A:L.96, A:W.227 Hydrogen bonds: A:A.200, A:S.205, A:G.228, A:G.230, A:G.230 Water bridges: A:S.205, A:W.227, A:E.229, A:Y.240 Salt bridges: A:H.43, A:D.199

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.4: 2 residues within 4Å: Chain A: P.48, N.53 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:P.48 Hydrogen bonds: A:N.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hilpert, K. et al., Design and Synthesis of Potent and Highly Selective Thrombin Inhibitors. J.Med.Chem. (1994)

Release Date

2012-06-20

Peptides

PROTHROMBIN: A
HIRUDIN VARIANT-1: B
PROTHROMBIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
I

C
L

PROTHROMBIN

HIRUDIN VARIANT-1

PROTHROMBIN

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